Setup

First, load the libraries needed for the workflow

library(tidyverse)
library(CoRC)

Input

Put in all variables needed to customise the workflow

Put in the path to the model (SBML), as url or local path (as string) and load the model. Use loadModel() for .cps models.

modelPathSBML <- "./Models/Leloup2004Circadian_model.xml"
loadSBML(modelPathSBML)
#> # A COPASI model reference:
#> Model name: "Leloup2004 - Mammalian Circadian Rhythm models for 23.8 and 24.2 hours timeperiod"
#> Number of compartments: 1
#> Number of species: 19
#> Number of reactions: 48

Load the data into the variable data.

data <- read.csv("./Data/Leloup2004Circadian_data.csv", sep = "")

Define experiment(s) for Parameter Estimation. For multiple experiments use list of defineExperiments().

experiment <- defineExperiments(
  data = data,
  type = c("time", "dependent", "dependent", "dependent", "dependent", "dependent", "dependent"),
  mapping = c(NA, getSpeciesReferences(key = c("MP", "MC", "MB", "PTot", "CTot", "BTot"))$concentration),
  weight_method = "mean_square"
)

Set Parameter Estimation Parameters. For more parameters, copy the defineParameterEstimationParameter() function and append the list. All parameters in this model are mapped to global Quantities. For Parameter Estimation, the Global Quantities not assigned or with an ode (so only “fixed” global Quantities) are estimated.

globalQ <- getGlobalQuantities()[getGlobalQuantities()$type == "fixed",]$key
lapply(globalQ, add_pe_param_global, lower = 100, upper = 100)
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Set Parameter Estimation Settings.

setParameterEstimationSettings(
  method = "LevenbergMarquardt"
)

Set Sigma Point Method Settings. Choose alpha, beta, kappa, and the measurement error (var)

alpha <- 1
beta <- 2
kappa <- 0
measurement_error <- 0.05

Do you want to save the result as a RDS object? Also give the file, where you want to save it.

save <- TRUE
file <- "docs/SP_Leloup"

Workflow

This should generally not need to be changed, only if the workflow is to be changed more generally.

result <-
  runSigmaPoint(
    alpha             = alpha,
    beta              = beta,
    kappa             = kappa,
    var               = measurement_error,
    experiments       = experiment,
    mean_fit_as_basis = TRUE,
  )

if (save){
  saveRDS(result, 
          file = file)
}

Output

This workflow produces the following output:

result$sp_mean
#>   Values[vmP].InitialValue  Values[kdmp].InitialValue   Values[KAP].InitialValue 
#>                1.101504744                0.003451218                0.714878225 
#>   Values[KmP].InitialValue   Values[vmC].InitialValue  Values[kdmc].InitialValue 
#>                0.365326811                0.990230227                0.011315345 
#>   Values[KAC].InitialValue   Values[KmC].InitialValue   Values[vmB].InitialValue 
#>                0.587155824                0.427851568                0.768961853 
#>  Values[kdmb].InitialValue   Values[KIB].InitialValue   Values[KmB].InitialValue 
#>                0.007101126                2.164843436                0.841746130 
#>    Values[k1].InitialValue    Values[k2].InitialValue    Values[k3].InitialValue 
#>                0.431505382                0.200771061                0.293499161 
#>    Values[k4].InitialValue    Values[k5].InitialValue    Values[k6].InitialValue 
#>                0.210254502                0.385797339                0.187131010 
#>    Values[k7].InitialValue    Values[k8].InitialValue  Values[kdnc].InitialValue 
#>                0.790218122                0.313895046                0.132251954 
#>   Values[kdn].InitialValue Values[kstot].InitialValue     Values[m].InitialValue 
#>                0.004577419                0.997737634                1.483688042 
#>     Values[n].InitialValue Values[vstot].InitialValue    Values[Kd].InitialValue 
#>                6.880430384                0.972988762                0.281510483 
#>   Values[Kdp].InitialValue    Values[Kp].InitialValue Values[Vphos].InitialValue 
#>                0.217435602                0.106819657                0.406600990 
#>   Values[V1B].InitialValue   Values[V1C].InitialValue   Values[V2B].InitialValue 
#>                0.525223406                0.468599275                0.108969896 
#>   Values[V2C].InitialValue   Values[V2P].InitialValue  Values[V2PC].InitialValue 
#>               -0.044763959                0.304847956                0.166897312 
#>   Values[V3B].InitialValue   Values[V4B].InitialValue  Values[V4PC].InitialValue 
#>                0.439097722                0.236139676                0.245730456 
#>  Values[vdBC].InitialValue  Values[vdBN].InitialValue  Values[vdCC].InitialValue 
#>               -0.102842238                0.712961988                0.797071944 
#>  Values[vdIN].InitialValue  Values[vdPC].InitialValue Values[vdPCC].InitialValue 
#>                1.619296051                0.711853066                0.583241870 
#> Values[vdPCN].InitialValue 
#>                1.426045246
result$sp_cov_matrix
#>                            Values[vmP].InitialValue Values[kdmp].InitialValue
#> Values[vmP].InitialValue               1.640030e-03              0.0001967238
#> Values[kdmp].InitialValue              1.967238e-04              0.0005644759
#> Values[KAP].InitialValue              -4.771169e-04             -0.0005700953
#> Values[KmP].InitialValue              -4.674045e-03             -0.0048999256
#> Values[vmC].InitialValue               7.788995e-04              0.0013369198
#> Values[kdmc].InitialValue              5.951593e-04              0.0004578829
#> Values[KAC].InitialValue               2.928525e-04             -0.0001348343
#> Values[KmC].InitialValue              -1.734717e-03             -0.0019300259
#> Values[vmB].InitialValue               1.707357e-03              0.0022244241
#> Values[kdmb].InitialValue              1.107572e-04              0.0001656489
#> Values[KIB].InitialValue               8.899279e-03              0.0129312552
#> Values[KmB].InitialValue              -3.103139e-02             -0.0378921558
#> Values[k1].InitialValue               -3.385650e-04              0.0001647050
#> Values[k2].InitialValue               -4.743382e-03             -0.0063010067
#> Values[k3].InitialValue                3.738589e-03              0.0039002896
#> Values[k4].InitialValue                6.542612e-04              0.0011626005
#> Values[k5].InitialValue                7.276377e-04              0.0008645500
#> Values[k6].InitialValue                2.939448e-04              0.0006283965
#> Values[k7].InitialValue               -1.759883e-02             -0.0240077444
#> Values[k8].InitialValue               -7.179371e-03             -0.0154549988
#> Values[kdnc].InitialValue             -3.901189e-04             -0.0004725572
#>                            Values[KAP].InitialValue Values[KmP].InitialValue
#> Values[vmP].InitialValue              -0.0004771169            -0.0046740452
#> Values[kdmp].InitialValue             -0.0005700953            -0.0048999256
#> Values[KAP].InitialValue               0.0029027577             0.0065751012
#> Values[KmP].InitialValue               0.0065751012             0.0694482114
#> Values[vmC].InitialValue              -0.0014281400            -0.0142958878
#> Values[kdmc].InitialValue             -0.0005814399            -0.0057138134
#> Values[KAC].InitialValue               0.0010220657            -0.0020026852
#> Values[KmC].InitialValue               0.0008359858             0.0208143406
#> Values[vmB].InitialValue              -0.0026620202            -0.0261898533
#> Values[kdmb].InitialValue             -0.0002117754            -0.0019641838
#> Values[KIB].InitialValue              -0.0132155660            -0.1520117914
#> Values[KmB].InitialValue               0.0432727595             0.4430988840
#> Values[k1].InitialValue               -0.0003730674             0.0005495606
#> Values[k2].InitialValue                0.0089292068             0.0729326016
#> Values[k3].InitialValue               -0.0056945050            -0.0529917424
#> Values[k4].InitialValue                0.0006830092             0.0008569212
#> Values[k5].InitialValue               -0.0005099632            -0.0108442910
#> Values[k6].InitialValue               -0.0008727875            -0.0076190932
#> Values[k7].InitialValue                0.0288730162             0.2792492413
#> Values[k8].InitialValue                0.0192067577             0.1753984341
#> Values[kdnc].InitialValue              0.0005005619             0.0057820606
#>                            Values[vmC].InitialValue Values[kdmc].InitialValue
#> Values[vmP].InitialValue               0.0007788995              5.951593e-04
#> Values[kdmp].InitialValue              0.0013369198              4.578829e-04
#> Values[KAP].InitialValue              -0.0014281400             -5.814399e-04
#> Values[KmP].InitialValue              -0.0142958878             -5.713813e-03
#> Values[vmC].InitialValue               0.0038870627              1.173256e-03
#> Values[kdmc].InitialValue              0.0011732564              7.925043e-04
#> Values[KAC].InitialValue              -0.0004520536             -1.651658e-05
#> Values[KmC].InitialValue              -0.0057532594             -1.239134e-03
#> Values[vmB].InitialValue               0.0059157159              2.403898e-03
#> Values[kdmb].InitialValue              0.0004391074              1.769555e-04
#> Values[KIB].InitialValue               0.0334974941              1.396566e-02
#> Values[KmB].InitialValue              -0.1008145359             -4.109984e-02
#> Values[k1].InitialValue                0.0003311778             -2.712440e-04
#> Values[k2].InitialValue               -0.0169339838             -6.495013e-03
#> Values[k3].InitialValue                0.0104640979              5.030229e-03
#> Values[k4].InitialValue                0.0032734386              5.988324e-04
#> Values[k5].InitialValue                0.0023848978              9.941486e-04
#> Values[k6].InitialValue                0.0016823887              8.690512e-04
#> Values[k7].InitialValue               -0.0638248271             -2.553062e-02
#> Values[k8].InitialValue               -0.0392172298             -1.568026e-02
#> Values[kdnc].InitialValue             -0.0014278882             -8.103785e-04
#>                            Values[KAC].InitialValue Values[KmC].InitialValue
#> Values[vmP].InitialValue               2.928525e-04            -0.0017347168
#> Values[kdmp].InitialValue             -1.348343e-04            -0.0019300259
#> Values[KAP].InitialValue               1.022066e-03             0.0008359858
#> Values[KmP].InitialValue              -2.002685e-03             0.0208143406
#> Values[vmC].InitialValue              -4.520536e-04            -0.0057532594
#> Values[kdmc].InitialValue             -1.651658e-05            -0.0012391344
#> Values[KAC].InitialValue               2.530224e-03             0.0004808342
#> Values[KmC].InitialValue               4.808342e-04             0.0145154574
#> Values[vmB].InitialValue               9.092004e-06            -0.0092509396
#> Values[kdmb].InitialValue             -1.414516e-05            -0.0006875667
#> Values[KIB].InitialValue               1.628013e-03            -0.0520224854
#> Values[KmB].InitialValue              -2.201875e-03             0.1574282123
#> Values[k1].InitialValue               -7.752998e-04            -0.0006237093
#> Values[k2].InitialValue                1.412651e-03             0.0266045750
#> Values[k3].InitialValue                8.775389e-04            -0.0133784943
#> Values[k4].InitialValue               -3.785711e-03            -0.0009726257
#> Values[k5].InitialValue                5.216902e-04            -0.0038542223
#> Values[k6].InitialValue                1.376628e-04            -0.0016151382
#> Values[k7].InitialValue                5.420146e-04             0.0982026580
#> Values[k8].InitialValue                1.549894e-03             0.0572231919
#> Values[kdnc].InitialValue              4.450054e-04             0.0019912999
#>                            Values[vmB].InitialValue Values[kdmb].InitialValue
#> Values[vmP].InitialValue               1.707357e-03              1.107572e-04
#> Values[kdmp].InitialValue              2.224424e-03              1.656489e-04
#> Values[KAP].InitialValue              -2.662020e-03             -2.117754e-04
#> Values[KmP].InitialValue              -2.618985e-02             -1.964184e-03
#> Values[vmC].InitialValue               5.915716e-03              4.391074e-04
#> Values[kdmc].InitialValue              2.403898e-03              1.769555e-04
#> Values[KAC].InitialValue               9.092004e-06             -1.414516e-05
#> Values[KmC].InitialValue              -9.250940e-03             -6.875667e-04
#> Values[vmB].InitialValue               1.159712e-02              8.710251e-04
#> Values[kdmb].InitialValue              8.710251e-04              6.862704e-05
#> Values[KIB].InitialValue               6.886700e-02              5.088751e-03
#> Values[KmB].InitialValue              -1.959841e-01             -1.425939e-02
#> Values[k1].InitialValue                2.361248e-04              2.539470e-05
#> Values[k2].InitialValue               -3.227009e-02             -2.428410e-03
#> Values[k3].InitialValue                2.184215e-02              1.640493e-03
#> Values[k4].InitialValue                3.768756e-04             -1.353109e-05
#> Values[k5].InitialValue                4.640330e-03              3.462186e-04
#> Values[k6].InitialValue                3.657756e-03              2.869445e-04
#> Values[k7].InitialValue               -1.210570e-01             -9.108611e-03
#> Values[k8].InitialValue               -7.566605e-02             -5.750267e-03
#> Values[kdnc].InitialValue             -2.465701e-03             -1.863503e-04
#>                            Values[KIB].InitialValue Values[KmB].InitialValue
#> Values[vmP].InitialValue                0.008899279             -0.031031388
#> Values[kdmp].InitialValue               0.012931255             -0.037892156
#> Values[KAP].InitialValue               -0.013215566              0.043272760
#> Values[KmP].InitialValue               -0.152011791              0.443098884
#> Values[vmC].InitialValue                0.033497494             -0.100814536
#> Values[kdmc].InitialValue               0.013965658             -0.041099837
#> Values[KAC].InitialValue                0.001628013             -0.002201875
#> Values[KmC].InitialValue               -0.052022485              0.157428212
#> Values[vmB].InitialValue                0.068867004             -0.195984067
#> Values[kdmb].InitialValue               0.005088751             -0.014259393
#> Values[KIB].InitialValue                0.577084900             -1.177937453
#> Values[KmB].InitialValue               -1.177937453              3.382519408
#> Values[k1].InitialValue                 0.004519981             -0.003192034
#> Values[k2].InitialValue                -0.176319409              0.545054189
#> Values[k3].InitialValue                 0.120589842             -0.369020101
#> Values[k4].InitialValue                 0.007425274             -0.011005147
#> Values[k5].InitialValue                 0.027918949             -0.078892985
#> Values[k6].InitialValue                 0.017483113             -0.059371782
#> Values[k7].InitialValue                -0.700540285              2.045841426
#> Values[k8].InitialValue                -0.456717185              1.271907004
#> Values[kdnc].InitialValue              -0.014862278              0.041556033
#>                            Values[k1].InitialValue Values[k2].InitialValue
#> Values[vmP].InitialValue             -3.385650e-04           -0.0047433822
#> Values[kdmp].InitialValue             1.647050e-04           -0.0063010067
#> Values[KAP].InitialValue             -3.730674e-04            0.0089292068
#> Values[KmP].InitialValue              5.495606e-04            0.0729326016
#> Values[vmC].InitialValue              3.311778e-04           -0.0169339838
#> Values[kdmc].InitialValue            -2.712440e-04           -0.0064950127
#> Values[KAC].InitialValue             -7.752998e-04            0.0014126513
#> Values[KmC].InitialValue             -6.237093e-04            0.0266045750
#> Values[vmB].InitialValue              2.361248e-04           -0.0322700894
#> Values[kdmb].InitialValue             2.539470e-05           -0.0024284105
#> Values[KIB].InitialValue              4.519981e-03           -0.1763194091
#> Values[KmB].InitialValue             -3.192034e-03            0.5450541889
#> Values[k1].InitialValue               1.784283e-03           -0.0005302363
#> Values[k2].InitialValue              -5.302363e-04            0.1040947941
#> Values[k3].InitialValue              -6.818670e-04           -0.0628380035
#> Values[k4].InitialValue               3.356606e-03           -0.0064765193
#> Values[k5].InitialValue              -2.501045e-04           -0.0124862631
#> Values[k6].InitialValue              -3.239268e-04           -0.0095872610
#> Values[k7].InitialValue              -3.005106e-03            0.3375970464
#> Values[k8].InitialValue              -3.814519e-03            0.2007052367
#> Values[kdnc].InitialValue             3.470799e-04            0.0063203356
#>                            Values[k3].InitialValue Values[k4].InitialValue
#> Values[vmP].InitialValue              0.0037385894            6.542612e-04
#> Values[kdmp].InitialValue             0.0039002896            1.162600e-03
#> Values[KAP].InitialValue             -0.0056945050            6.830092e-04
#> Values[KmP].InitialValue             -0.0529917424            8.569212e-04
#> Values[vmC].InitialValue              0.0104640979            3.273439e-03
#> Values[kdmc].InitialValue             0.0050302289            5.988324e-04
#> Values[KAC].InitialValue              0.0008775389           -3.785711e-03
#> Values[KmC].InitialValue             -0.0133784943           -9.726257e-04
#> Values[vmB].InitialValue              0.0218421523            3.768756e-04
#> Values[kdmb].InitialValue             0.0016404926           -1.353109e-05
#> Values[KIB].InitialValue              0.1205898419            7.425274e-03
#> Values[KmB].InitialValue             -0.3690201005           -1.100515e-02
#> Values[k1].InitialValue              -0.0006818670            3.356606e-03
#> Values[k2].InitialValue              -0.0628380035           -6.476519e-03
#> Values[k3].InitialValue               0.0544301822            5.014691e-03
#> Values[k4].InitialValue               0.0050146911            1.085884e-01
#> Values[k5].InitialValue               0.0088386021            2.923591e-05
#> Values[k6].InitialValue               0.0071369950            1.659816e-03
#> Values[k7].InitialValue              -0.2290995942            6.808221e-03
#> Values[k8].InitialValue              -0.1466035433           -8.280477e-03
#> Values[kdnc].InitialValue            -0.0047542691            9.313237e-04
#>                            Values[k5].InitialValue Values[k6].InitialValue
#> Values[vmP].InitialValue              7.276377e-04            2.939448e-04
#> Values[kdmp].InitialValue             8.645500e-04            6.283965e-04
#> Values[KAP].InitialValue             -5.099632e-04           -8.727875e-04
#> Values[KmP].InitialValue             -1.084429e-02           -7.619093e-03
#> Values[vmC].InitialValue              2.384898e-03            1.682389e-03
#> Values[kdmc].InitialValue             9.941486e-04            8.690512e-04
#> Values[KAC].InitialValue              5.216902e-04            1.376628e-04
#> Values[KmC].InitialValue             -3.854222e-03           -1.615138e-03
#> Values[vmB].InitialValue              4.640330e-03            3.657756e-03
#> Values[kdmb].InitialValue             3.462186e-04            2.869445e-04
#> Values[KIB].InitialValue              2.791895e-02            1.748311e-02
#> Values[KmB].InitialValue             -7.889298e-02           -5.937178e-02
#> Values[k1].InitialValue              -2.501045e-04           -3.239268e-04
#> Values[k2].InitialValue              -1.248626e-02           -9.587261e-03
#> Values[k3].InitialValue               8.838602e-03            7.136995e-03
#> Values[k4].InitialValue               2.923591e-05            1.659816e-03
#> Values[k5].InitialValue               2.845808e-03            1.832540e-03
#> Values[k6].InitialValue               1.832540e-03            3.593006e-03
#> Values[k7].InitialValue              -4.877440e-02           -3.566099e-02
#> Values[k8].InitialValue              -2.872040e-02           -2.257393e-02
#> Values[kdnc].InitialValue            -1.055301e-03           -8.675964e-04
#>                            Values[k7].InitialValue Values[k8].InitialValue
#> Values[vmP].InitialValue             -0.0175988320            -0.007179371
#> Values[kdmp].InitialValue            -0.0240077444            -0.015454999
#> Values[KAP].InitialValue              0.0288730162             0.019206758
#> Values[KmP].InitialValue              0.2792492413             0.175398434
#> Values[vmC].InitialValue             -0.0638248271            -0.039217230
#> Values[kdmc].InitialValue            -0.0255306205            -0.015680255
#> Values[KAC].InitialValue              0.0005420146             0.001549894
#> Values[KmC].InitialValue              0.0982026580             0.057223192
#> Values[vmB].InitialValue             -0.1210570455            -0.075666051
#> Values[kdmb].InitialValue            -0.0091086110            -0.005750267
#> Values[KIB].InitialValue             -0.7005402853            -0.456717185
#> Values[KmB].InitialValue              2.0458414257             1.271907004
#> Values[k1].InitialValue              -0.0030051062            -0.003814519
#> Values[k2].InitialValue               0.3375970464             0.200705237
#> Values[k3].InitialValue              -0.2290995942            -0.146603543
#> Values[k4].InitialValue               0.0068082214            -0.008280477
#> Values[k5].InitialValue              -0.0487743984            -0.028720399
#> Values[k6].InitialValue              -0.0356609891            -0.022573929
#> Values[k7].InitialValue               1.3089366113             0.826794158
#> Values[k8].InitialValue               0.8267941581             0.727513226
#> Values[kdnc].InitialValue             0.0270928486             0.016196851
#>                            Values[kdnc].InitialValue Values[kdn].InitialValue
#> Values[vmP].InitialValue               -0.0003901189             2.268696e-04
#> Values[kdmp].InitialValue              -0.0004725572             2.018907e-04
#> Values[KAP].InitialValue                0.0005005619            -2.210499e-04
#> Values[KmP].InitialValue                0.0057820606            -2.574329e-03
#> Values[vmC].InitialValue               -0.0014278882             5.846383e-04
#> Values[kdmc].InitialValue              -0.0008103785             2.292922e-04
#> Values[KAC].InitialValue                0.0004450054             3.363037e-05
#> Values[KmC].InitialValue                0.0019912999            -1.006793e-03
#> Values[vmB].InitialValue               -0.0024657009             1.067071e-03
#> Values[kdmb].InitialValue              -0.0001863503             8.030861e-05
#> Values[KIB].InitialValue               -0.0148622785             5.715329e-03
#> Values[KmB].InitialValue                0.0415560326            -1.804661e-02
#> Values[k1].InitialValue                 0.0003470799            -3.535087e-05
#> Values[k2].InitialValue                 0.0063203356            -3.277567e-03
#> Values[k3].InitialValue                -0.0047542691             1.966715e-03
#> Values[k4].InitialValue                 0.0009313237            -5.655168e-05
#> Values[k5].InitialValue                -0.0010553012             4.701193e-04
#> Values[k6].InitialValue                -0.0008675964             2.588697e-04
#> Values[k7].InitialValue                 0.0270928486            -1.137009e-02
#> Values[k8].InitialValue                 0.0161968509            -6.103530e-03
#> Values[kdnc].InitialValue               0.0015760912            -2.541832e-04
#>                            Values[kstot].InitialValue Values[m].InitialValue
#> Values[vmP].InitialValue                -1.134492e-04           0.0171641143
#> Values[kdmp].InitialValue                3.424773e-04           0.0239330027
#> Values[KAP].InitialValue                -3.790871e-04          -0.0271190560
#> Values[KmP].InitialValue                -2.863969e-03          -0.2768947382
#> Values[vmC].InitialValue                 7.725894e-04           0.0633607015
#> Values[kdmc].InitialValue                1.355702e-04           0.0250347255
#> Values[KAC].InitialValue                -1.698914e-05          -0.0007327001
#> Values[KmC].InitialValue                -1.371361e-03          -0.1020096675
#> Values[vmB].InitialValue                 1.346584e-03           0.1242318825
#> Values[kdmb].InitialValue                9.966793e-05           0.0093543114
#> Values[KIB].InitialValue                 8.235181e-03           0.6870023602
#> Values[KmB].InitialValue                -2.312244e-02          -2.0936915339
#> Values[k1].InitialValue                  9.897290e-05           0.0004038621
#> Values[k2].InitialValue                 -4.499747e-03          -0.3490293025
#> Values[k3].InitialValue                  2.340413e-03           0.2358687793
#> Values[k4].InitialValue                 -1.540082e-03           0.0085231688
#> Values[k5].InitialValue                  8.149080e-04           0.0503432361
#> Values[k6].InitialValue                  4.746142e-05           0.0396514221
#> Values[k7].InitialValue                 -1.593697e-02          -1.2889216477
#> Values[k8].InitialValue                 -9.686605e-03          -0.8170956473
#> Values[kdnc].InitialValue               -6.622050e-05          -0.0258920885
#>                            Values[n].InitialValue Values[vstot].InitialValue
#> Values[vmP].InitialValue              0.135567981               0.0027712777
#> Values[kdmp].InitialValue             0.082986905               0.0029318068
#> Values[KAP].InitialValue             -0.044362578              -0.0034929599
#> Values[KmP].InitialValue             -0.870338979              -0.0352946669
#> Values[vmC].InitialValue              0.145481545               0.0080060314
#> Values[kdmc].InitialValue             0.094420549               0.0032746032
#> Values[KAC].InitialValue              0.145750434               0.0001766008
#> Values[KmC].InitialValue             -0.237401866              -0.0125797690
#> Values[vmB].InitialValue              0.290836817               0.0151486688
#> Values[kdmb].InitialValue             0.020411368               0.0011284522
#> Values[KIB].InitialValue              2.036780046               0.0838210365
#> Values[KmB].InitialValue             -5.191463523              -0.2571825233
#> Values[k1].InitialValue              -0.044047924               0.0001595672
#> Values[k2].InitialValue              -0.882874781              -0.0429892666
#> Values[k3].InitialValue               0.568458181               0.0290471549
#> Values[k4].InitialValue               1.161392326               0.0006543794
#> Values[k5].InitialValue               0.175740175               0.0061432547
#> Values[k6].InitialValue              -0.007318833               0.0047814131
#> Values[k7].InitialValue              -3.528843507              -0.1597273587
#> Values[k8].InitialValue              -3.426533089              -0.0964735315
#> Values[kdnc].InitialValue            -0.033423018              -0.0032234487
#>                            Values[Kd].InitialValue Values[Kdp].InitialValue
#> Values[vmP].InitialValue              9.441290e-04             2.462906e-05
#> Values[kdmp].InitialValue             5.430144e-04            -4.407883e-03
#> Values[KAP].InitialValue             -1.680887e-03             4.014793e-03
#> Values[KmP].InitialValue             -8.216578e-03             5.221407e-02
#> Values[vmC].InitialValue              1.547780e-03            -1.124316e-02
#> Values[kdmc].InitialValue             7.509288e-04            -4.282797e-03
#> Values[KAC].InitialValue              1.635511e-05            -1.472607e-03
#> Values[KmC].InitialValue             -2.427384e-03             1.471488e-02
#> Values[vmB].InitialValue              3.454270e-03            -2.189789e-02
#> Values[kdmb].InitialValue             2.727546e-04            -1.693490e-03
#> Values[KIB].InitialValue              1.075426e-02            -1.004314e-01
#> Values[KmB].InitialValue             -5.567041e-02             3.644737e-01
#> Values[k1].InitialValue               5.421195e-06             2.997637e-04
#> Values[k2].InitialValue              -1.110065e-02             5.822085e-02
#> Values[k3].InitialValue               9.134001e-03            -4.577389e-02
#> Values[k4].InitialValue              -1.197388e-02             5.093730e-03
#> Values[k5].InitialValue               6.711124e-04            -9.988636e-03
#> Values[k6].InitialValue               1.044643e-03            -9.199851e-03
#> Values[k7].InitialValue              -4.095996e-02             2.401285e-01
#> Values[k8].InitialValue              -2.724026e-02             1.623180e-01
#> Values[kdnc].InitialValue            -8.402471e-04             4.715819e-03
#>                            Values[Kp].InitialValue Values[Vphos].InitialValue
#> Values[vmP].InitialValue             -1.689635e-03               1.849401e-04
#> Values[kdmp].InitialValue            -2.322926e-03               9.121099e-04
#> Values[KAP].InitialValue              2.524297e-03              -1.246776e-03
#> Values[KmP].InitialValue              2.572162e-02              -1.026024e-02
#> Values[vmC].InitialValue             -6.141154e-03               2.339791e-03
#> Values[kdmc].InitialValue            -2.365979e-03               8.100724e-04
#> Values[KAC].InitialValue              2.709412e-05               1.951036e-04
#> Values[KmC].InitialValue              9.098553e-03              -3.638480e-03
#> Values[vmB].InitialValue             -1.126356e-02               4.875636e-03
#> Values[kdmb].InitialValue            -8.327923e-04               3.659444e-04
#> Values[KIB].InitialValue             -6.836245e-02               2.636870e-02
#> Values[KmB].InitialValue              1.922818e-01              -8.219219e-02
#> Values[k1].InitialValue              -7.008600e-04               3.977147e-05
#> Values[k2].InitialValue               3.052378e-02              -1.394238e-02
#> Values[k3].InitialValue              -2.130375e-02               9.539211e-03
#> Values[k4].InitialValue              -1.706720e-03              -1.994457e-03
#> Values[k5].InitialValue              -4.306907e-03               2.103232e-03
#> Values[k6].InitialValue              -3.438652e-03               1.819004e-03
#> Values[k7].InitialValue               1.213663e-01              -5.191061e-02
#> Values[k8].InitialValue               7.795059e-02              -3.504186e-02
#> Values[kdnc].InitialValue             2.405585e-03              -8.330632e-04
#>                            Values[V1B].InitialValue Values[V1C].InitialValue
#> Values[vmP].InitialValue              -0.0012935348              0.008046290
#> Values[kdmp].InitialValue             -0.0015673842              0.009861355
#> Values[KAP].InitialValue               0.0015542087             -0.011143817
#> Values[KmP].InitialValue               0.0191434044             -0.116877931
#> Values[vmC].InitialValue              -0.0042739285              0.027062012
#> Values[kdmc].InitialValue             -0.0017005524              0.010736545
#> Values[KAC].InitialValue              -0.0003669680             -0.001187301
#> Values[KmC].InitialValue               0.0068584815             -0.041950942
#> Values[vmB].InitialValue              -0.0082722237              0.049874793
#> Values[kdmb].InitialValue             -0.0006211625              0.003742148
#> Values[KIB].InitialValue              -0.0473655402              0.289270212
#> Values[KmB].InitialValue               0.1401350120             -0.844453057
#> Values[k1].InitialValue               -0.0000937286              0.001014750
#> Values[k2].InitialValue                0.0232327817             -0.138382283
#> Values[k3].InitialValue               -0.0159551108              0.097223739
#> Values[k4].InitialValue                0.0004578370              0.011785936
#> Values[k5].InitialValue               -0.0035355236              0.020771748
#> Values[k6].InitialValue               -0.0023161146              0.015375070
#> Values[k7].InitialValue                0.0881303652             -0.527509253
#> Values[k8].InitialValue                0.0552023789             -0.339663851
#> Values[kdnc].InitialValue              0.0017919421             -0.011984332
#>                            Values[V2B].InitialValue Values[V2C].InitialValue
#> Values[vmP].InitialValue               7.623156e-04              0.012908332
#> Values[kdmp].InitialValue              5.009783e-04              0.018707965
#> Values[KAP].InitialValue               2.337544e-04             -0.021458146
#> Values[KmP].InitialValue              -9.288457e-03             -0.213502820
#> Values[vmC].InitialValue               1.795522e-03              0.049164950
#> Values[kdmc].InitialValue              6.062570e-04              0.018601342
#> Values[KAC].InitialValue               9.008230e-04              0.001567361
#> Values[KmC].InitialValue              -4.330029e-03             -0.076894918
#> Values[vmB].InitialValue               3.550186e-03              0.092697103
#> Values[kdmb].InitialValue              2.641416e-04              0.006965007
#> Values[KIB].InitialValue               2.303340e-02              0.525865159
#> Values[KmB].InitialValue              -6.029040e-02             -1.567311047
#> Values[k1].InitialValue                9.067647e-05              0.002768138
#> Values[k2].InitialValue               -1.033873e-02             -0.257209297
#> Values[k3].InitialValue                5.719480e-03              0.176188310
#> Values[k4].InitialValue               -1.766556e-03              0.007230667
#> Values[k5].InitialValue                2.674320e-03              0.037659310
#> Values[k6].InitialValue                9.611723e-04              0.028794185
#> Values[k7].InitialValue               -3.613116e-02             -0.984228344
#> Values[k8].InitialValue                3.163777e-03             -0.627124205
#> Values[kdnc].InitialValue             -7.859350e-04             -0.019067066
#>                            Values[V2P].InitialValue Values[V2PC].InitialValue
#> Values[vmP].InitialValue                0.006413576              0.0030132547
#> Values[kdmp].InitialValue               0.008616843              0.0013083473
#> Values[KAP].InitialValue               -0.011119174             -0.0015745878
#> Values[KmP].InitialValue               -0.099989167             -0.0202599161
#> Values[vmC].InitialValue                0.023735722              0.0038152562
#> Values[kdmc].InitialValue               0.008424367              0.0022314123
#> Values[KAC].InitialValue               -0.001129459              0.0017038612
#> Values[KmC].InitialValue               -0.035357615             -0.0079058739
#> Values[vmB].InitialValue                0.042825793              0.0090008036
#> Values[kdmb].InitialValue               0.003188429              0.0006304260
#> Values[KIB].InitialValue                0.250330890              0.0640289855
#> Values[KmB].InitialValue               -0.726922024             -0.1586523144
#> Values[k1].InitialValue                 0.002173196             -0.0013735732
#> Values[k2].InitialValue                -0.123307423             -0.0249391428
#> Values[k3].InitialValue                 0.080627756              0.0161400127
#> Values[k4].InitialValue                 0.006558810              0.0132190810
#> Values[k5].InitialValue                 0.016598170              0.0055485961
#> Values[k6].InitialValue                 0.011895694              0.0045395148
#> Values[k7].InitialValue                -0.454892838             -0.0900845920
#> Values[k8].InitialValue                -0.284022524             -0.0619777097
#> Values[kdnc].InitialValue              -0.008592753             -0.0017233145
#>                            Values[V3B].InitialValue Values[V4B].InitialValue
#> Values[vmP].InitialValue               0.0042080665             1.370592e-03
#> Values[kdmp].InitialValue              0.0058760963            -5.302983e-04
#> Values[KAP].InitialValue              -0.0065356720             7.385265e-04
#> Values[KmP].InitialValue              -0.0682771955             4.487689e-03
#> Values[vmC].InitialValue               0.0157028447            -7.872808e-04
#> Values[kdmc].InitialValue              0.0060692531            -3.899043e-04
#> Values[KAC].InitialValue               0.0001647663             2.720735e-05
#> Values[KmC].InitialValue              -0.0249026837             4.975907e-04
#> Values[vmB].InitialValue               0.0295543064            -2.644792e-03
#> Values[kdmb].InitialValue              0.0022092803            -2.224484e-04
#> Values[KIB].InitialValue               0.1725527681            -1.309143e-02
#> Values[KmB].InitialValue              -0.5013902060             4.220815e-02
#> Values[k1].InitialValue                0.0007717008             1.447926e-05
#> Values[k2].InitialValue               -0.0834275214             5.246157e-03
#> Values[k3].InitialValue                0.0553247182            -5.309756e-03
#> Values[k4].InitialValue                0.0003510345             8.414038e-03
#> Values[k5].InitialValue                0.0118444049            -1.410603e-03
#> Values[k6].InitialValue                0.0081331693            -1.305798e-03
#> Values[k7].InitialValue               -0.3152691262             3.090544e-02
#> Values[k8].InitialValue               -0.1948834412             2.317422e-02
#> Values[kdnc].InitialValue             -0.0062954617             9.731323e-04
#>                            Values[V4PC].InitialValue Values[vdBC].InitialValue
#> Values[vmP].InitialValue               -0.0233239710              -0.012109507
#> Values[kdmp].InitialValue              -0.0275960801              -0.005844249
#> Values[KAP].InitialValue                0.0286589293               0.015755766
#> Values[KmP].InitialValue                0.3313004342               0.138122578
#> Values[vmC].InitialValue               -0.0742486255              -0.035823312
#> Values[kdmc].InitialValue              -0.0302930358              -0.013548851
#> Values[KAC].InitialValue               -0.0040311500               0.026792773
#> Values[KmC].InitialValue                0.1192468102               0.013080451
#> Values[vmB].InitialValue               -0.1422455203              -0.052888739
#> Values[kdmb].InitialValue              -0.0105923394              -0.004291050
#> Values[KIB].InitialValue               -0.8351794613              -0.325159255
#> Values[KmB].InitialValue                2.4162984706               0.855146854
#> Values[k1].InitialValue                -0.0009238571              -0.021143800
#> Values[k2].InitialValue                 0.3988206093               0.132029327
#> Values[k3].InitialValue                -0.2709650609              -0.167397436
#> Values[k4].InitialValue                -0.0118381494              -0.152304155
#> Values[k5].InitialValue                -0.0570791256              -0.007433783
#> Values[k6].InitialValue                -0.0418315004               0.001205591
#> Values[k7].InitialValue                 1.5043975043               0.510967277
#> Values[k8].InitialValue                 0.9541151203               0.216056538
#> Values[kdnc].InitialValue               0.0304053507               0.016569705
#>                            Values[vdBN].InitialValue Values[vdCC].InitialValue
#> Values[vmP].InitialValue               -0.0054789146              -0.004253473
#> Values[kdmp].InitialValue              -0.0055809172              -0.004976497
#> Values[KAP].InitialValue                0.0094883209               0.005850134
#> Values[KmP].InitialValue                0.0541763186               0.059231602
#> Values[vmC].InitialValue               -0.0137270923              -0.012345103
#> Values[kdmc].InitialValue              -0.0065140323              -0.003992791
#> Values[KAC].InitialValue                0.0058866914              -0.003612633
#> Values[KmC].InitialValue                0.0212667686               0.023221759
#> Values[vmB].InitialValue               -0.0240156654              -0.025454274
#> Values[kdmb].InitialValue              -0.0018262090              -0.001891768
#> Values[KIB].InitialValue               -0.1508041530              -0.150746705
#> Values[KmB].InitialValue                0.4044641299               0.434536627
#> Values[k1].InitialValue                -0.0036990523              -0.001280318
#> Values[k2].InitialValue                 0.0598927977               0.072830728
#> Values[k3].InitialValue                -0.0298334246              -0.047377880
#> Values[k4].InitialValue                 0.0064533259               0.005419520
#> Values[k5].InitialValue                -0.0065692534              -0.010690456
#> Values[k6].InitialValue                -0.0063115109              -0.005476985
#> Values[k7].InitialValue                 0.2558731583               0.266991245
#> Values[k8].InitialValue                 0.1351233462               0.173936658
#> Values[kdnc].InitialValue               0.0084197221               0.002007804
#>                            Values[vdIN].InitialValue Values[vdPC].InitialValue
#> Values[vmP].InitialValue                 0.017740501             -9.882288e-04
#> Values[kdmp].InitialValue                0.014431770             -1.136973e-03
#> Values[KAP].InitialValue                -0.014549178              5.946363e-04
#> Values[KmP].InitialValue                -0.193050251              2.998121e-02
#> Values[vmC].InitialValue                 0.044159170             -5.222519e-03
#> Values[kdmc].InitialValue                0.022127757             -2.874444e-03
#> Values[KAC].InitialValue                -0.007460657              2.004022e-04
#> Values[KmC].InitialValue                -0.051231790              5.995573e-03
#> Values[vmB].InitialValue                 0.076252686             -1.119229e-02
#> Values[kdmb].InitialValue                0.005941764             -8.356453e-04
#> Values[KIB].InitialValue                 0.396131756             -8.214434e-02
#> Values[KmB].InitialValue                -1.274084663              1.912991e-01
#> Values[k1].InitialValue                 -0.012616000              1.132619e-03
#> Values[k2].InitialValue                 -0.201423256              3.276954e-02
#> Values[k3].InitialValue                  0.168942091             -2.070627e-02
#> Values[k4].InitialValue                  0.003755973              4.031427e-03
#> Values[k5].InitialValue                  0.036181320             -3.677002e-03
#> Values[k6].InitialValue                  0.016818597             -3.376537e-03
#> Values[k7].InitialValue                 -0.845796533              1.163499e-01
#> Values[k8].InitialValue                 -0.440138261              1.065522e-01
#> Values[kdnc].InitialValue               -0.027426214              3.532267e-03
#>                            Values[vdPCC].InitialValue Values[vdPCN].InitialValue
#> Values[vmP].InitialValue                 0.0025012774               2.551235e-04
#> Values[kdmp].InitialValue                0.0047491914              -1.206112e-03
#> Values[KAP].InitialValue                -0.0062608687              -1.383645e-03
#> Values[KmP].InitialValue                -0.0501240255              -1.173265e-02
#> Values[vmC].InitialValue                 0.0125255446              -1.270760e-03
#> Values[kdmc].InitialValue                0.0045860017               8.040371e-04
#> Values[KAC].InitialValue                -0.0013668098               1.803948e-03
#> Values[KmC].InitialValue                -0.0175022422               3.569239e-03
#> Values[vmB].InitialValue                 0.0222046454               3.754089e-03
#> Values[kdmb].InitialValue                0.0016757915               3.167571e-04
#> Values[KIB].InitialValue                 0.1295885618               9.885311e-03
#> Values[KmB].InitialValue                -0.3736432318              -5.705298e-02
#> Values[k1].InitialValue                  0.0007412429              -2.425044e-03
#> Values[k2].InitialValue                 -0.0658037129              -1.179346e-02
#> Values[k3].InitialValue                  0.0444574398               7.057153e-03
#> Values[k4].InitialValue                  0.0158908112              -6.487370e-02
#> Values[k5].InitialValue                  0.0089643368              -3.009275e-03
#> Values[k6].InitialValue                  0.0065434740               2.453085e-03
#> Values[k7].InitialValue                 -0.2368821634              -3.913001e-02
#> Values[k8].InitialValue                 -0.1515363575              -2.690512e-02
#> Values[kdnc].InitialValue               -0.0052840400              -1.234632e-03
#>  [ erreichte getOption("max.print") --  25 Zeilen ausgelassen ]

Utils

add_pe_param_global <- function(name, upper, lower){
  value     <- getGlobalQuantities(key = name)$initial_value
  value_ref <- getGlobalQuantityReferences(key = name)$initial_value
  addParameterEstimationParameter(   ref         = value_ref,
                                     start_value = value,
                                     lower_bound = value-value*lower,
                                     upper_bound = value+value*upper)
}